How do I finish cutting out this wheel well?
I would suggest the Knife Project command.



Basically you choose the cutting object, than the object to cut, enter in edit mode, put the camera perpendicular to the projection plane (if the object is shrinkwrapped you just have to avoid to make all the cutting geometry to be visible from the cam) and run the command.

It will also automatically select the inner faces of the cutting loop.



Another could be to use boolean operations.

From the cutting profile you have to create some faces and extrude them just of the amount needed to penetrate the object to cut. Than apply Boolean modifier set to Difference



Once applied, you should have the faces that belonged to the cutting object extrusion selected, ready to be deleted.